Index

_

__init__() (open3SPN2.System method)

A

Angle (class in open3SPN2)

B

BasePair (class in open3SPN2)

Bond (class in open3SPN2)

C

CoarseGrain() (open3SPN2.DNA static method) computeGeometry() (open3SPN2.DNA method)

computeTopology() (open3SPN2.DNA method) CrossStacking (class in open3SPN2)

D

Dihedral (class in open3SPN2)

DNA (class in open3SPN2) DNATypeError (class in open3SPN2)

E

Electrostatics (class in open3SPN2) ElectrostaticsProteinDNA (class in open3SPN2)

Exclusion (class in open3SPN2) ExclusionProteinDNA (class in open3SPN2)

F

Feynman fixPDB() (in module open3SPN2) fromCoarsePDB() (open3SPN2.DNA class method)

fromPDB() (open3SPN2.DNA class method) fromSequence() (open3SPN2.DNA class method) fromXYZ() (open3SPN2.DNA class method)

G

getSequences() (open3SPN2.DNA method)

P

parseConfigTable() (in module open3SPN2) parseConfigurationFile() (open3SPN2.DNA method)

parsePDB() (in module open3SPN2) pdb2table() (in module open3SPN2)

S

Stacking (class in open3SPN2)

System (class in open3SPN2)

T

test_DNA_from_xyz() (in module open3SPN2) test_parse_log() (in module open3SPN2)

test_parse_xyz() (in module open3SPN2) TestEnergies (class in open3SPN2)

W

writePDB() (open3SPN2.DNA method)